Construction of a foxtail millet linkage map and mapping of spikelet-tipped bristles 1(stb1) by using transposon display markers and simple sequence repeat markers with genome sequence information

We attempted genetic analysis and mapping of a gene responsible for the trait “spikelet-tipped bristles” (stb) in foxtail millet, Setaria italica (L.) P.Beauv., as the first step in positional cloning of the gene. This trait is important not only in grain yield such as grain number per panicle of this millet but also in the evolutionary development of the “bristle grass” clade including genera Setaria, Pennisetum and Cenchrus in subfamily Panicoideae. First of all, we confirmed that this trait is controlled by a single recessive gene, using two populations of F2 plants; one was a cross combination between two Taiwanese landraces and the other was a combination between a Taiwanese landrace and a Japanese landrace. Using the latter of the two F2 populations, with transposon display (TD) markers and simple sequence repeat (SSR) markers developed previously, we constructed a genetic map with 13 linkage groups and mapped the responsible gene (stb1) on chromosome 2. We also developed novel SSR markers by using foxtail millet genome sequence information, and we finally constructed nine linkage groups corresponding to nine chromosomes with a total length of 1287.5 cM, and mapped stb1 more precisely on chromosome 2. This work suggests that the foxtail millet genome sequences recently published are useful for developing genome-wide SSR markers for constructing linkage maps and mapping genes in this millet.     

Comparative genetic maps of foxtail millet (Setaria italica) and rice (Oryza sativa)

 A foxtail millet-rice comparative genetic map was constructed using mapped rice RFLP markers and wheat genomic and cDNA clones with known map position in rice. About 74% and 37% of the cDNA and genomic clones, respectively, were transferable to foxtail millet, confirming that conservation at the DNA level is greatest in genic regions. A high degree of conserved colinearity was observed between the two genomes. Five entire foxtail millet chromosomes appear to be colinear with five entire rice chromosomes. The remaining four foxtail millet linkage groups each show colinearity with segments of two rice chromosomes. The rearrangements of rice chromosomes 3 and 10 to form foxtail millet chromosome IX, and 7 and 9 to form chromosome II are very similar to those required to form maize chromosomes 1 and 7 and sorghum linkage groups C and B, indicating Setaria’s clear taxonomic position within the subfamily of the Panicoideae. Received: 18 December 1996 / Accepted: 4 August 1997     

Phytolith analysis for differentiating between foxtail millet (Setaria italica) and green foxtail (Setaria viridis)

Foxtail millet (Setaria italica) is one of the oldest domesticated cereal crops in Eurasia, but identifying foxtail millets, especially in charred grains, and differentiating it from its wild ancestor, green foxtail (Setaria viridis), in the archaeobotanical remains, is still problematic. Phytolithic analysis provides a meaningful method for identifying this important crop. In this paper, the silicon structure patterns in the glumes, lemmas, and paleas from inflorescence bracts in 16 modern plants of foxtail millet and green foxtail from China and Europe are examined using light microscopy with phase-contrast and a microscopic interferometer. Our research shows that the silicon structure of ΩIII from upper lemmas and paleas in foxtail millet and green foxtail can be correspondingly divided into two groups. The size of ΩIII type phytolith of foxtail millet is bigger than that from green foxtail. Discriminant function analysis reveals that 78.4% of data on foxtail millet and 76.9% of data on green foxtail are correctly classified. This means certain morphotypes of phytoliths are relatively reliable tools for distinguishing foxtail millet from green foxtail. Our results also revealed that the husk phytolith morphologies of foxtail millets from China and Eastern Europe are markedly different from those from Western Europe. Our research gives a meaningful method of separating foxtail millet and green foxtail. The implications of these findings for understanding the history of foxtail millet domestication and cultivation in ancient civilizations are significant.     

Genetic structure of landraces in foxtail millet (Setaria italica (L.) P. Beauv.) revealed with transposon display and interpretation to crop evolution of foxtail millet

Although the origin and domestication process of foxtail millet (Setaria italica subsp. italica (L.) P. Beauv.) has been studied by several groups, the issue is still ambiguous. It is essential to resolve this issue by studying a large number of accessions with sufficient markers covering the entire genome. Genetic structures were analyzed by transposon display (TD) using 425 accessions of foxtail millet and 12 of the wild ancestor green foxtail (Setaria italica subsp. viridis (L.) P. Beauv.). We used three recently active transposons (TSI-1, TSI-7, and TSI-10) as genome-wide markers and succeeded in demonstrating geographical structures of the foxtail millet. A neighbor-joining dendrogram based on TD grouped the foxtail millet accessions into eight major clusters, each of which consisted of accessions collected from adjacent geographical areas. Eleven out of 12 green foxtail accessions were grouped separately from the clusters of foxtail millet. These results indicated strong regional differentiations and a long history of cultivation in each region. Furthermore, we discuss the relationship between foxtail millet and green foxtail and suggest a monophyletic origin of foxtail millet domestication.     

Genome sequence of foxtail millet (Setaria italica) provides insights into grass evolution and biofuel potential

Foxtail millet (Setaria italica), a member of the Poaceae grass family, is an important food and fodder crop in arid regions and has potential for use as a C(4) biofuel. It is a model system for other biofuel grasses, including switchgrass and pearl millet. We produced a draft genome (～423 Mb) anchored onto nine chromosomes and annotated 38,801 genes. Key chromosome reshuffling events were detected through collinearity identification between foxtail millet, rice and sorghum including two reshuffling events fusing rice chromosomes 7 and 9, 3 and 10 to foxtail millet chromosomes 2 and 9, respectively, that occurred after the divergence of foxtail millet and rice, and a single reshuffling event fusing rice chromosome 5 and 12 to foxtail millet chromosome 3 that occurred after the divergence of millet and sorghum. Rearrangements in the C(4) photosynthesis pathway were also identified.     

抗、感黑穗病谷子品种几种酶活性的比较研究

本文对7个不同抗、感黑穗病的谷子品种在不同时期进行了超氧化物歧化酶、过氧化物酶、多酚氧化酶活性的比较研究。结果表明,谷子感染黑穗病后,体内超氧化物歧化酶、过氧化物酶、多酚氧化酶活性均显著增强。抗病品种的酶活性明显地高于感病品种。这些酶活性的变化能够削弱或消除病菌对谷子的毒害作用,在谷子抗黑穗病过程中发挥重要作用。     

Ribosomal DNA intergenic spacer sequence in foxtail millet, Setaria italica (L.) P. Beauv. and its characterization and application to typing of foxtail millet landraces

We determined the sequence of ribosomal DNA (rDNA) intergenic spacer (IGS) of foxtail millet isolated in our previous study, and identified subrepeats in the polymorphic region. We also developed a PCR-based method for identifying rDNA types based on sequence information and assessed 153 accessions of foxtail millet. Results were congruent with our previous works. This study provides new findings regarding the geographical distribution of rDNA variants. This new method facilitates analyses of numerous foxtail millet accessions. It is helpful for typing of foxtail millet germplasms and elucidating the evolution of this millet.     

用gFM31探针进行谷子品种的指纹分析

用高度多态性探针ｇＦＭ３１对５９个谷子（ＳｅｔａｒｉａｉｔａｒｌｉｃａＢｅａｕｖ．）品种（包括地方品种、育成品种及品系）进行ＤＮＡ指纹分析,共鉴别出５８种类型,而黑谷和黑粒１５１６给出完全相同的带型,二者有可能是同一材料。通过对ｇＦＭ３１ＤＮＡ序列分析,未发现其中有小卫星ＤＮＡ和微卫星ＤＮＡ序列。该探针虽在谷子品种中显示很高的多态性,但与禾谷类的其他物种的ＤＮＡ杂交信号微弱,表现出较强的谷子基因组特异性。     

2,4-D和干燥处理对谷子成熟胚离体再生体系的影响

谷子离体再生体系不够稳定、转化效率低，已成为谷子功能基因研究和品种改良的瓶颈。为了建立谷子成熟胚稳定的离体再生体系，以当地高产优质的6个谷子品种成熟胚为外植体，以不同2,4-二氯苯氧乙酸（2,4-dichlorophenoxyacetic acid，2,4-D）浓度及对胚性愈伤的不同干燥处理时间为变量，通过单因素实验和正交实验考察各因素对谷子愈伤组织分化及成苗的影响。结果表明，晋谷21在2,4-D浓度为9 μmol·L-1、4 h干燥处理的条件下所建立的再生体系最好，分化率为64.35%，成苗率为29.06%。研究通过探索谷子组织培养的最适条件，为谷子高效稳定遗传转化体系的建立和利用基因工程手段进行品质改良提供了依据。     

中国禾谷类作物野生近缘植物在育种中的利用

中国主要禾谷类作物有水稻、小麦、大麦、燕麦、玉米、高粱、粟、黍稷,它们的野生近缘植物在中国禾谷类作物育种中得到了较好的利用,不仅拓宽了作物的遗传基础,而且培育出优良品种在生产上大面积推广,在提高粮食产量中起到了重要作用.     

Comparative mapping reveals a complex relationship between the pearl millet genome and those of foxtail millet and rice

Comparative genetic maps were constructed of the pearl millet genome with foxtail millet and used to describe the homoeology between the genomes of pearl millet, foxtail millet and rice. Despite the close taxonomic relationship of pearl and foxtail millet, their genomes were highly, rearranged. A comparison of the millet and rice genomes indicated that most of these rearrangements were likely to have taken place in pearl millet. Two duplications were identified in pearl millet. A duplication between the distal segments of linkage groups 1 and 4 corresponds to the ancient duplication previously identified between rice chromosome arms 11S and 12S and foxtail millet chromosomes VII and VIII. The other putative duplication, also between regions of linkage groups 1 and 4, is likely to be species-specific. The exploitation of the comparative maps in pearl millet research is discussed. Received: 10 February 1999 / Accepted: 6 July 1999     

Study of genetic diversity and relationships among accessions of foxtail millet [Setaria italica (L.) P. Beauv.] in Korea, China, and Pakistan using SSR markers

In this study, 28 simple sequence repeat (SSR) primer sets were used to analyze the genetic diversity, population structure, and genetic relationships among 37 accessions of foxtail millet from Korea, China and Pakistan. A total of 298 alleles were detected with an average allele number of 10.6 per locus among 37 foxtail millet accessions. The number of alleles per locus ranged from 2 (b226) to 20 (b236). Of the 298 alleles, 138 alleles (46.3%) were rare (frequency < 0.05), 152 alleles (51.0%) were detected at an intermediate frequency (range, 0.05?C0.50), and eight alleles (2.7%) were abundant (frequency > 0.50), respectively. The average gene diversity values were 0.652, 0.692, and 0.491 and polymorphic information content values were 0.621, 0.653, and 0.438, for accessions from Korea, China, and Pakistan, respectively. The accessions from China showed higher SSR diversity than those from Korea and Pakistan. A phylogenetic tree constructed using the un-weighted pair group methods with arithmetic mean algorithm revealed three major groups of accessions that were not congruent with geographical distribution patterns with a few exceptions. The lack of correlation between the accession clusters and their geographic location indicates that the diffusion of foxtail millet from China to Korea might have occurred through multiple routes. Our results provide support for the origin and diffusion route of foxtail millet in East Asia. This SSR-based assessment of genetic diversity, genetic relationships, and population structure among genetic resources of foxtail millet landraces will be valuable to foxtail millet breeding and genetic conservation programs in Korea.     

中国谷子潜在地理分布的多模型比较

谷子是中国干旱和半干旱区主要的粮食作物之一.它耐旱、耐瘠薄、抗逆性强、适应性广,是未来应对干旱形势的重要战略储备作物.本文基于谷子的157个地理分布点数据,利用中国谷子产量与环境指标的相关性分析,选出10个气候指标、7个土壤指标和3个地形指标,采用MaxEnt、EMFA、RF和GAM共4个物种分布模型,分析中国谷子的潜在适宜性分布.结果表明: 4种模型均可成功模拟谷子的潜在地理分布,其中,MaxEnt模型的模拟效果最好.选用的环境指标中,水热条件对谷子生长最敏感.模型结果结合ArcGIS空间分析模块的结果表明,中国谷子的潜在适宜生长区(最适宜区和适宜区)总面积为55.68×10⁴ km²,远远大于当前谷子的实际种植面积,主要集中在东北地区的东北平原、长白山以南与牡丹江流域,华北地区的淮河以北,华中地区汉江以东与大别山以北,西北地区的黄土高原、鄂尔多斯高原南部、祁连山脉东部、天山山脉东部与阿尔泰山脉,西南地区的重庆以北和贵州西部局地区域.     

郑州东赵遗址炭化植物遗存记录的夏商时期农业特征及其发展过程

本文通过对郑州东赵遗址2013~2014年度考古发掘采集土样的浮选分析,获取了该遗址新砦、二里头、二里岗三个不同时期丰富的炭化植物遗存,其中炭化植物种子主要包括粟、黍、水稻、小麦和大豆五种农作物以及狗尾草属、稗属和马唐属等不同种属的杂草种子等。对遗址不同阶段炭化农作物及典型田间杂草遗存的量化分析结果显示,东赵遗址自新砦期至二里岗期的农业生产始终保持着以种植粟、黍为主的特点,大豆是该遗址先民稳定的食物来源之一,而水稻在整个农业经济结构中的比重一直很低。值得注意的是,从新砦期至二里岗期,粟、黍两种旱地作物在东赵遗址农业经济中的比重不断上升,而先民的旱地田间管理技术也随之取得了明显的进步。小麦的种植始于遗址二里头文化期,至二里岗期时迅速发展,成为当时先民重要的农作物品种之一。东赵遗址炭化植物遗存分析结果为了解夏代早期至商代前期中原核心区域农业经济的特点及其发展过程提供了重要资料,对探索中国国家起源与早期发展阶段农业经济技术发展状况及其与文明演进的关系有重要意义。     

Development of 5123 Intron-Length Polymorphic Markers for Large-Scale Genotyping Applications in Foxtail Millet

Generating genomic resources in terms of molecular markers is imperative in molecular breeding for crop improvement. Though development and application of microsatellite markers in large-scale was reported in the model crop foxtail millet, no such large-scale study was conducted for intron-length polymorphic (ILP) markers. Considering this, we developed 5123 ILP markers, of which 4049 were physically mapped onto 9 chromosomes of foxtail millet. BLAST analysis of 5123 expressed sequence tags (ESTs) suggested the function for ∼71.5% ESTs and grouped them into 5 different functional categories. About 440 selected primer pairs representing the foxtail millet genome and the different functional groups showed high-level of cross-genera amplification at an average of ∼85% in eight millets and five non-millet species. The efficacy of the ILP markers for distinguishing the foxtail millet is demonstrated by observed heterozygosity (0.20) and Nei''s average gene diversity (0.22). In silico comparative mapping of physically mapped ILP markers demonstrated substantial percentage of sequence-based orthology and syntenic relationship between foxtail millet chromosomes and sorghum (∼50%), maize (∼46%), rice (∼21%) and Brachypodium (∼21%) chromosomes. Hence, for the first time, we developed large-scale ILP markers in foxtail millet and demonstrated their utility in germplasm characterization, transferability, phylogenetics and comparative mapping studies in millets and bioenergy grass species.     

The archaeobotanical significance of immature millet grains: an experimental case study of Chinese millet crop processing

We present evidence from ethnography and experimental processing of foxtail millet (Setaria italica (L.) P. Beauv.) in China that spikelets containing incompletely filled (or immature) grains constitute a significant portion of typical millet harvests and are removed along with other by-products after threshing and winnowing. This study provides a baseline for the identification of immature foxtail grains in archaeobotanical assemblages. Immature millet grains are a frequent component of archaeobotanical assemblages in Neolithic and Bronze Age China, and criteria for their recognition are presented based on our modern experimental result and illustrated with archaeobotanical examples from Shandong and Henan. It is seed morphology rather than size that plays a determinative role in the identification of foxtail millet. It is suggested that those grains with a narrow egg-shaped embryo, which is about 5/6 of the whole grain, and having a round shape can be classed as foxtail millet even though they are small, flat and squashed. While different grades of immaturity in millet grains might be defined, the interpretative potential of these appears to be negligible as all immature grains are concentrated in winnowing waste. This study confirms the suggestion that the ratio of immature to mature millet grains can be employed in archaeobotany in considering whether or not early stage crop processing (threshing and winnowing) contributed to the formation of particular archaeological millet assemblages.     

利用野生青狗尾草的细胞质培育谷子质核互作雄性不育材料

利用野生青狗尾草N10为母本,谷子农家品种大青秸为父本,进行种间杂交,获得了3株杂种。杂种在农艺性状上表现为谷子和青狗尾草的种间类型,花器表现了雄性败育,但雌蕊发育正常,能接受外来花粉结实。细胞形态学观察表明,其雄性败育表现为单核小孢子典败。该谷子雄性不育材料的获得,为利用野生青狗尾草的细胞质培育谷子质核互作雄性不育系,进而为实现谷子三系配套杂种优势利用奠定了基础。     

谷子穗分化的扫描电镜观察

利用扫描电镜对复合品种冀谷１１号的穗分化进行了系统观察,比较了夏谷和春谷穗分化的异同。提出了谷子穗分化划分为穗分化前期、生长锥伸长期、枝梗分化期、小穗和刚毛分化期以及小花分化期共５个时期,就谷子刚毛起源穗分化与栽培育种的关系等问题进行了讨论。     

谷子（Setaria italica）分子遗传研究进展

近年来不断发展和完善的生物技术为谷子的研究开辟了新的思路,且提供了新的手段。本文概述了谷子在分子标记、遗传图谱的构建、基因定位、功能蛋白基因的克隆、转基因技术等方面的研究进展,提出了谷子分子遗传研究中存在的问题,并对今后的发展趋势作了初步探讨。     

Construction and application of EST library from Setaria italica in response to dehydration stress

Foxtail millet is a gramineous crop with low water requirement. Despite its high water use efficiency, less attention has been paid to the molecular genetics of foxtail millet. This article reports the construction of subtracted cDNA libraries from foxtail millet seedlings under dehydration stress and the expression profile analysis of 1947 UniESTs from the subtracted cDNA libraries by a cDNA microarray. The results showed that 95 and 57 ESTs were upregulated by dehydration stress, respectively, in roots and shoots of seedlings and that 10 and 27 ESTs were downregulated, respectively, in roots and shoots. The expression profile analysis showed that genes induced in foxtail millet roots were different from those in shoots during dehydration stress and that the early response to dehydration stress in foxtail millet roots was the activation of the glycolysis metabolism. Moreover, protein degradation pathway may also play a pivotal role in drought-tolerant responses of foxtail millet. Finally, Northern blot analysis validated well the cDNA microarray data.